Handel Package
From Biowiki
Handel Package
Handel: an evolutionary model-based Statistical Alignment package.
- Main program:
- handalign - program to sample multiple alignments, phylogenies, and parameters. Currently the main supported program in the Handel package. See HandAlign transducer for a depiction of the underlying model.
- Input:
- handalign - program to sample multiple alignments, phylogenies, and parameters. Currently the main supported program in the Handel package. See HandAlign transducer for a depiction of the underlying model.
* either unaligned sequences (Fasta Format), or (optionally) an alignment (Stockholm Format) which may include an embedded tree (Newick Format) * optional rate matrix (Xrate Format)
- Output:
* final or best alignment (Stockholm Format) with embedded tree (Newick Format) and model parameters * (optionally) an MCMC sampling trace of all alignments/trees/parameters visited (Stockholm Format + Newick Format)
- Utility programs:
- Stockholm Tools - utilities for working with files in Stockholm Format
- phylocomposer - program for analysis using String Transducers. Can be used to reproduce the individual sampling steps of handalign.
- Input: tree, transducer composition file (Phylo Composer format -- a derivative of Lisp S Expressions)
- Output: composite & acyclic transducers, alignments (Phylo Composer format)
- phylodirector.pl - program for visualizing state paths through String Transducers
- Input: alignment (Stockholm Format)
- Output: movie file (MPEG Format); still image files (PNG Format & SVG Format)
- Older programs in the package:
- tkfemit - program to sample multiple alignments from the prior implied by the TKF91 model and a given phylogenetic tree
- Input: tree (Newick Format), optional rate matrix (Xrate Format)
- Output: alignment (Stockholm Format)
- tkfdistance - program to estimate distance matrices using the TKF91 model
- Input: either sequences (Fasta Format) or an alignment (Stockholm Format)
- Output: distance matrix (Distance Format)
- tkfalign - MCMC phylogenetic alignment package using TKF91
- Input: tree (Newick Format), optional rate matrix (Xrate Format), and either sequences (Fasta Format) or an alignment (Stockholm Format)
- Output: alignment(s) (Stockholm Format)
- See Why MCMCIs Networking For Modelers for discussion of why the MCMC functionality is cool
- tkfemit - program to sample multiple alignments from the prior implied by the TKF91 model and a given phylogenetic tree
Related programs in DART...
- StemLoc, Evol Doer: multiple alignment of RNA
- Input: either sequences (Fasta Format) or alignments (Stockholm Format)
- Output: alignment(s) (Stockholm Format)
- xrate: mutation rate measurement using EM algorithm (Xrate Format, Stockholm Format)
- xfold, xprot and xgram: multiple alignment annotation using evolutionary SCFGs (Xgram Format, Stockholm Format)
Background...
- See Phylogenetic Alignment Reader for more background info and context on Phylo Alignment
- a good review is Lunter et al.: Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 2005;6:83.
- See Multiple RNAAlignment for papers and theory relating to multiple alignment of RNA
Getting in touch...
